Input mtDNA variants in any of the 7 major formats, mixed formats input is supported. The results are returned as multiple html tables, as well as a downloadable combined Excel file. An API is implemented, which takes inputs in VCF, HGVS, or classical mtDNA variant nomenclatures, and returns annotated vcf or json outputs.

VariantOneStop is updated with dbNSFP v3.4, notably added CADD, M-CAP and REVEL scores, ExAC and 1000Gp3 population allele frequencies, conservation scores enhanced to 100way.
VariantOneStop is updated with population frequency data from Genome Aggregation Database (gnomAD), The data set spans 123,136 exomes and 15,496 genomes from unrelated individuals sequenced as part of various disease-specific and population genetic studies.

2017-03-30

MSeqDR HPO Browser is enhanced to always show 5 levels in ontology tree, HPO database is updated to 201701 release.

HPO Browser is enhanced to always show 5 levels in tree, rather than the previous 3 levels: Grandparent, parent, self, child, grand child. Terms are shown with full HPO name in grand child.

Expert Panel Recruiting: MSeqDr is organizing an expert panel for mitochondrial diseases and pathogenic variants. Welcome to share your expertise. Please visit the site to see current panel members, tools and documents.

Abstract

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.

MSeqDR.org will serve as a permanent site to host the pathogenic
variants associated with manuscripts to "CSH Molecular Case
Studies".

Novel disease genes and variants can be added to MSeqDR-LSDB.
A custom MSeqDR accession number is assigned to all annotated
pathogenic variants that are either submitted by users or batch
extracted from other databases such as ClinVar or Ensembl, each
containing a unique MSCV (MSeqDR Clinically-related Variant)
identifier with a 7-digit code. Users can readily submit
variants, in either VCF or HGVS formats, using the custom
MSeqDR ‘Pathogenic variant submission tool’
(https://mseqdr.org/submission.php)

2016-02-09

Project Update:
MSeqDR-Genesis and Dr. Marni Falk are featured in the 2015
CHOP Annual Report, The Children's Hospital of
Philadelphia .

It's also highlighted in the CSO's last bullet point:

"Find out how a curious researcher contemplating a seemingly
unsolvable patient case can reach out to another investigator on
the opposite side of the world studying a patient with a similar
genetic makeup. Working together, in a matter of minutes they
can pinpoint the genetic mutations that may explain the rare
disease that their patients have in common".

Project Update: Phy-Mer, MSeqDR's own
haplogroup classifier tool is running as web-based service in
MSeqDR. Phy-Mer is a novel alignment-free and
reference-independent tool, and it supports input in fasta,
fastq, bam, csv formats.

2015-01-09

Project Update:
LSDB is upgraded to LOVD 3.0.12, which restored the gene and
variant creation funtions that rely on Mutalyzer webservice.

2014-11-25

Publication:The
first paper describing the MSeqDR Project is accepted for
publication:

MSeqDR server is migrated to MEEI, Harvard University. A new
domain name for the project: https:/MSeqdr.org.

Human Phenotype Ontology support is being implemented. Search by
accession# or keywords at: HPO Search, and at
top search box (prefix keywords with "PH:").

2014-01-16

Project Update:

Two major variation tracks are added. The were provided by HmtDB Project lead by Dr. Marcella Attimonelli. HmtDB is a Human
Mitochondrial Genomic Resource Based on Variability Studies
Supporting Population Genetics and Biomedical Research.

The data are derived from a pool of 1000 healthy and about
2000 patient genomes annotated in HmtDB. The tracks have been
produced according to rCRS and RSRS.

The HBCR annotation is updated to dbSNP138.

2013-12-03

Project Update:

MSeqDR-LSDB, the Mitochondrial Disease Locus Specific Database, is open
to the public. It is a major effort in promoting information
integration and sharing.

This LSDB is integrating phenotyping and variation data from
multiple comprehensive or disease specific resources, including
clinVar, MITOMAP, Ensembl phenotype, and OMIM. It will focus on genes
involved in mitochondrial diseases, whose products are located
in mitochondrian, and mitochondrial genome. The clinical,
genetics, and variants information will be available. The LSDB
is based on LOVD (v3.0.08)
with extensive in-house customizations and enhancements.

2013-11-26

Project Update: Phenotype
associated variants are added as new tracks in Gbrowse, and
available from our new MSeqDR-LSDB. The
information were compiled from clinVar, MITOMAP , and Ensembl .

Project Update: We
are delighted that the aggregated variantion data for NuclearMitome
Comprehensive Sequence Analysis of 448 Nuclear Mitochondrial
Genes from Transgenomic
Inc., is available at MSeqDR. Interested users please
contact the company for access request. The dataset has ~108K
variants from 151 patients, targeting 448 candidate genes for
mitochondrial disease.

2013-11-25

Project Update: WebEx
discussion between MSeqDR, MITOMAP
and HmtDB on
collaborating in bring together tools and data for
mitochondrial research.